The primary goal of this study is to characterize on a genomic scale the adaptive evolution of Escherichia coli clones in the course of long-term urinary tract infections (UTI), in particular, episodes of recurrent cystitis and UTI characterized by a shift between the asymptomatic and symptomatic state. The main hypothesis to be tested is that adaptive evolution of uropathogenic E. coli is among the key mechanisms underlying the shift from the acute form of UTIs to recurrent infection and from asymptomatic to symptomatic infection. Molecular adaptation of bacterial pathogens in the course of infection involves point mutations in structural or regulatory genes as well as deletion or duplication of whole genes or chromosomal regions. These pathogenicity-adaptive mutations can confer a selective advantage by improving the ability of the bacteria to adhere to or invade the uroepithelium or evade host defenses. There is strong evidence from both published and our preliminary studies that E. coli undergoes pathogenicity-adaptive evolution in the course of recurrent or long-term UTI. The studies proposed here will expand our understanding of this phenomena to the genomic level by employing two novel technologies, high-density microarrays and a whole-genome mutation scan developed in our laboratory. Both of these technologies will be utilized to perform a comparative analysis of sequential or matching clones of E. coli that have been isolated from patients with long-term UTI or in a chronic animal model of UTI. We will also define how adaptive evolution of uropathogens affects their ability to bind and invade uroepithelial cells, resist cellular host defenses and colonize in a mouse model of UTI. We expect that the proposed studies will clarify the mechanisms of long-term adaptive evolution of uropathogenic E. coli and provide a basis for future studies directed at a detailed understanding of the molecular pathogenesis of persistent and recurrent UTIs.